9EI7

PasI from Photorhabdus asymbiotica bound to vanadyl, succinate, and 5-amino-6-hydroxy-octanosyl acid 2-phosphate

This is a non-PDB format compatible entry.

Summary for 9EI7

• Entry DOI: 10.2210/pdb9ei7/pdb
• Descriptor: Prolyl 4-hydroxylase alpha subunit domain-containing protein, 1-(5-amino-3,7-anhydro-5-deoxy-2-O-phosphono-D-threo-beta-D-allo-octofuranuronosyl)pyrimidine-2,4(1H,3H)-dione, GLYCEROL, ... (7 entities in total)
• Functional Keywords: iron, polyoxin, biosynthesis, vanadyl, nucleotide, high-carbon sugar, oxygen, oxidoreductase
• Biological source: Photorhabdus asymbiotica
• Total number of polymer chains: 1
• Total formula weight: 27148.74

Authors

Dong, J.,Boal, A.K.,Lin, C.-Y. (deposition date: 2024-11-25, release date: 2025-08-20, Last modification date: 2025-08-27)

Primary citation

Du, Y.,Dong, J.,Draelos, M.M.,Collazo-Perez, L.N.,Majer, S.H.,Boal, A.K.,Yokoyama, K.
Unusual O-H Activation-Initiated C-C Bond Cleavage Reaction by a Nonheme Fe Enzyme in Antifungal Nucleoside Biosynthesis.
J.Am.Chem.Soc., 147:30163-30177, 2025

PubMed Abstract: Fe(II)- and α-ketoglutarate (α-KG)-dependent enzymes catalyze diverse reactions, generally initiated by Fe=O mediated cleavage of C-H bonds with bond dissociation energies (BDE) of up to ∼100 kcal/mol. Here, we report the discovery of a novel reaction initiated by a significantly more challenging O-H bond cleavage (>100 kcal/mol). This activity was identified in PolD, an enzyme that regulates the sugar size in antifungal nucleoside biosynthesis by catalyzing the transformation of a bicyclic eight-carbon sugar substrate, 5'-amino-6'-hydroxy-octosyl acid 2'-phosphate (AHOAP), into a monocyclic six-carbon product, aminohexuronic acid 2'-phosphate (AHAP). Our studies demonstrate that PolD catalyzes a two-step reaction, in which AHOAP is first oxidized to 5'-amino-6'-keto-octosyl acid 2'-phosphate (AKOAP) via typical C-H activation, followed by a unique C-C bond cleavage on AKOAP to AHAP initiated by O-H activation. X-ray crystal structures of PolD and its homologue, PasI, the latter solved in complex with AHOAP, succinate, and vanadyl, a structural mimic of the Fe-oxo intermediate, reveal a substrate binding mode that is consistent with both C-H and O-H homolysis. A comparison of the three enzymes, PasI, PolD, and MalI, all of which exhibit distinct C-C bond cleavage activities, suggests that precise substrate positioning to bring the target OH group of AKOAP close to the Fe-oxo intermediate is critical for hydrogen atom transfer from this functional group. These results indicate a novel reactivity of the Fe═O intermediate in Fe/α-KG enzymes, thereby expanding the reaction scope of this enzyme superfamily. The results also reveal the molecular mechanism of the divergent biosynthesis of antifungal nucleosides.

PubMed: 40787846
DOI: 10.1021/jacs.5c08400

Experimental method

X-RAY DIFFRACTION (1.48 Å)